Laboratory for Complex Tissue Analysis

Victor G. Puelles

Mission Statement

“To decode pathological tissues across biological scales, paving the way to better diagnosis, stratification and treatment of patients”

— Victor G. Puelles, MD/PhD

Team Members


Milagros Wong, MD

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MD Student

Stefanie Graefe


Thiago Strieder

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Post Doc

Yusuke Okabayashi, MD/PhD

Clinician Scientist

Dominik Kylies, MD

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Clinician Scientist

Jan Czogalla, MD

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PhD student

Maria Schwerk

PhD student

Nico Kaiser

Research Associate

Malte Kuehl


The laboratory for complex tissue analysis focuses on the development and application of tissue-based technologies to dissect pathophysiological processes in a well-characterized spatial context which can be defined at different biological scales, including whole organs, intact functional structures, cells, and subcellular compartments.

Here, we provide some examples of the technologies available in our team:

  1. Optical clearing and light sheet microscopy: mammalian organs can be made translucent and advanced light microscopy can be used to visualize whole organs, ranging from mice to humans.
  2. Multiplex imaging: formalin-fixed paraffin-embedded (FFPE) tissues can be used to perform integrative anatomical and molecular analyses. We have developed a method for protein iterative staining and imaging, which can be combined with fluorescent in situ hybridization and classical histopathology. So far, we have been able to integrate over 60 markers in the same piece of tissue.
  3. Nanopathology: FFPE tissues can also be used to study subcellular structures at nanoscale (25-40nm), using a combination of expansion microscopy, bioinformatic image resolution enhancement, and LED-based widefield microscopy.
  4. Advanced image analysis: we use multiple tools, from classical segmentation to pixel-based cluster analysis and deep learning-based algorithms.

While our primary research goals are oriented towards understanding kidney disease, our technologies are applicable to any organ/system. At the moment, we have active collaborations in the fields of virology (eg. COVID-19), neurobiology (eg. cerebral malaria), gastroenterology (eg. immune-mediated colon and liver disorders), endocrinology (eg. obesity and diabetes), and hematology (eg. bone marrow fibrosis).

Victor Puelles, MD/PhD

Professor for Complex Tissue Analysis

III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE)
Martinistr. 52
20246 Hamburg, Germany

Department of Clinical Medicine, Aarhus University, and Department of Pathology, Aarhus University Hospital
Palle Juul-Jensens Boulevard 69, 8200 Aarhus N, Denmark


Current Position
since 2022

Professor for Complex Tissue Analysis, III. Department of Medicine, UKE, Hamburg, Gemany

since 2022 Professor for Complex Tissue Analysis, Department of Clinical Medicine, AU, Aarhus, Denmark    
University Training
2002 - 2009

MD, Universidad Peruana Cayetano Heredia, Peru

Academic qualifications
2011 - 2014 - 2020

PhD, Department of Anatomy and Developmental Biology, Monash University, Australia

Previous professional career

Scientific postgraduate education:

2020 - 2022

Group Leader and Assistant Professorship for Complex Tissue Analysis, III. Department of Medicine, UKE, Gemany

2018 - 2019

Humboldt Research Fellow, III. Department of Medicine, UKE, Germany

2016 - 2017

NHMRC CJ Martin Research Fellow, Department of Nephrology and Clinical Immunology, University Hospital RWTH Aachen, Germany

2015 - 2016 Research Fellow, Department of Anatomy and Developmental Biology, Monash University, Australia

Selected publications

Kylies D, Zimmermann M, Haas F, Schwerk M, Kuehl M, Brehler M, Czogalla J, Hernandez LC, Konczalla L, Okabayashi Y, Menzel J, Edenhofer I, Mezher S, Aypek H, Dumoulin B, Wu H, Hofmann S, Kretz O, Wanner N, Tomas NM, Krasemann S, Glatzel M, Kuppe C, Kramann R, Banjanin B, Schneider RK, Urbschat C, Arck P, Gagliani N, van Zandvoort M, Wiech T, Grahammer F, Sáez PJ, Wong MN, Bonn S, Huber TB, Puelles VG. Nat Nanotechnol. 2023 Apr;18(4):336-342. 

Molecular consequences of SARS-CoV-2 liver tropism.
Wanner N*, Andrieux G*, Badia-I-Mompel P, Edler C, Pfefferle S, Lindenmeyer MT, Schmidt-Lauber C, Czogalla J, Wong MN, Okabayashi Y, Braun F, Lütgehetmann M, Meister E, Lu S, Noriega MLM, Günther T, Grundhoff A, Fischer N, Bräuninger H, Lindner D, Westermann D, Haas F, Roedl K, Kluge S, Addo MM, Huber S, Lohse AW, Reiser J, Ondruschka B, Sperhake JP, Saez-Rodriguez J, Boerries M, Hayek SS, Aepfelbacher M, Scaturro P*, Puelles VG*, Huber TB*. Nat Metab. 2022, 4(3):310-319.


Pro-cachectic factors link experimental and human chronic kidney disease to skeletal muscle wasting programs.
Solagna F, Tezze C, Lindenmeyer MT, Lu S, Wu G, Liu S, Zhao Y, Mitchell R, Meyer C, Omairi S, Kilic T, Paolini A, Ritvos O, Pasternack A, Matsakas A, Kylies D, Wiesch JSZ, Turner JE, Wanner N, Nair V, Eichinger F, Menon R, Martin IV, Klinkhammer BM, Hoxha E, Cohen CD, Tharaux PL, Boor P, Ostendorf T, Kretzler M, Sandri M, Kretz O, Puelles VG*, Patel K*, Huber TB*. J Clin Invest. 2021, 131(11):e135821


Deep learning-based molecular morphometrics in kidney biopsies.
Zimmermann M*, Klaus M*, Wong MN, Thebille AK, Gernhold L, Kuppe C, Halder M, Kranz J, Wanner N, Braun F, Wulf S, Wiech T, Panzer U, Krebs CF, Hoxha E, Kramann R, Huber TB*, Bonn S*, Puelles VG*. JCI Insight. 2021, 6(7):e144779.


Decoding myofibroblast origins in human kidney fibrosis.
Kuppe C*, Ibrahim MM*, Kranz J, Zhang X, Ziegler S, Perales-Patón J, Jansen J, Reimer KC, Smith JR, Dobie R, Wilson-Kanamori JR, Halder M, Xu Y, Kabgani N, Kaesler N, Klaus M, Gernhold L, Puelles VG, Huber TB, Boor P, Menzel S, Hoogenboezem RM, Bindels EMJ, Steffens J, Floege J, Schneider RK, Saez-Rodriguez J, Henderson NC*, Kramann R*. Nature. 2021, 589(7841):281-286


SARS-CoV-2 renal tropism associates with acute kidney injury.
Braun F*, Lütgehetmann M*, Pfefferle S*, Wong MN*, Carsten A, Lindenmeyer MT, Nörz D, Heinrich F, Meißner K, Wichmann D, Kluge S, Gross O, Pueschel K, Schröder AS, Edler C*, Aepfelbacher M*, Puelles VG*, Huber TB*. Lancet. 2020, 396(10251):597-598


Multi-organ and renal tropism of SARS-CoV-2.
Puelles VG*, Lütgehetmann M*, Lindenmeyer MT*, Sperhake JP*, Wong MN, Allweiss L, Chilla S, Heinemann A, Wanner N, Liu S, Braun F, Lu S, Pfefferle S, Schröder AS, Edler C, Gross O, Glatzel M, Wichmann D, Wiech T, Kluge S, Pueschel K, Aepfelbacher M, Huber TB. N Engl J Med. 2020, 383(6):590-592.


Cellular and Molecular Probing of Intact Human Organs.
Zhao S, Todorov MI, Cai R, -Maskari RA, Steinke H, Kemter E, Mai H, Rong Z, Warmer M, Stanic K, Schoppe O, Paetzold JC, Gesierich B, Wong MN, Huber TB, Duering M, Bruns OT, Menze B, Lipfert J, Puelles VG, Wolf E, Bechmann I, Ertürk A. Cell. 2020, 180(4):796-812.e19.


mTOR-mediated podocyte hypertrophy regulates glomerular integrity in mice and humans.
Puelles VG, van der Wolde JW, Wanner N, Scheppach MW, Cullen-McEwen LA, Bork T, Lindenmeyer MT, Gernhold L, Wong MN, Braun F, Cohen CD, Kett MM, Kuppe C, Kramann R, Saritas T, van Roeyen CR, Moeller MJ, Tribolet L, Rebello R, Sun YB, Li J, Müller-Newen G, Hughson MD, Hoy WE, Person F, Wiech T, Ricardo SD, Kerr PG, Denton KM, Furic L, Huber TB, Nikolic-Paterson DJ, Bertram JF. JCI Insight. 2019, 4(18):e99271.


The tetraspanin CD9 controls invasive migration and proliferation of parietal epithelial cells and glomerular disease progression
Lazareth H*, Henique C*, Lenoir O*, Puelles VG*, Flamant M, Bollée G, Fligny C, Camus M, Guyonnet L, Millien C, Gaillard F, Chipont A, Robin B, Fabrega S, Dhaun N, Camerer E, Kretz O, Grahammer F, Braun F, Huber TB, Nochy D, Mandet C, Bruneval P, Mesnard L, Thervet E, Karras A, Le Naour F, Rubinstein E, Boucheix C, Alexandrou A, Moeller MJ, Bouzigues C, Tharaux PL. Nat Commun. 2019, 10(1):3303.

* Represents equal contributions as co-first or co-senior authors.



Open Positions

We are looking for highly motivated and ambitious postdocs, PhD students, master students, and student research assistants.

July 9, 2024 | Seminar
Open Positions

We are constantly looking for highly motivated, talented and team-oriented researchers to join our team ...

Martinistraße 52
Campus Research N27
20246 Hamburg Germany
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University Medical Center Hamburg - Eppendorf